Contacts of the helix formed by residues 38 - 54 (chain A) in PDB entry 1X3O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLY 3.4 3.2 + - - +
37A ALA* 1.3 73.1 - - - +
39A SER* 1.3 65.2 + - - +
40A LEU* 3.2 11.2 + - - +
41A ASP* 2.9 36.4 + - - +
42A THR* 3.0 24.7 + - - -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 1.3 74.1 - - - +
40A LEU* 1.3 62.8 + - - +
42A THR* 3.2 15.7 + - - -
43A VAL* 3.4 13.7 + - - +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 3.2 11.2 + - - +
39A SER* 1.3 77.7 - - - +
41A ASP* 1.3 67.1 + - - +
43A VAL* 3.2 16.1 - - + +
44A GLU* 3.0 45.5 + - + +
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Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS 3.6 16.9 - - - +
18A LEU* 3.9 20.5 - - + +
36A GLY 4.2 3.3 - - - +
37A ALA* 3.7 15.1 - - + -
38A ASP* 2.9 43.0 + - - +
40A LEU* 1.3 81.9 - - - +
42A THR* 1.3 57.9 + - - +
44A GLU* 3.7 6.3 - - - +
45A LEU* 2.8 32.8 + - - +
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 6.0 1.7 - - + +
32A ILE* 5.3 7.1 - - - +
37A ALA* 4.2 13.0 + - - +
38A ASP 3.0 15.2 + - - -
39A SER* 3.2 11.9 + - - -
41A ASP* 1.3 76.9 - - - +
43A VAL* 1.3 62.9 + - - +
45A LEU* 3.7 6.7 - - - +
46A ILE* 3.2 30.9 + - + +
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER 3.4 8.9 + - - +
40A LEU* 3.2 25.1 - - + +
42A THR* 1.3 77.4 - - - +
44A GLU* 1.3 70.1 + - + +
46A ILE* 3.4 6.6 + - + +
47A MET* 3.0 47.0 + - + +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 3.3 45.8 - - + +
40A LEU* 3.0 42.2 + - + +
41A ASP* 3.7 7.6 - - - +
43A VAL* 1.3 82.3 - - + +
45A LEU* 1.3 56.9 + - - +
47A MET* 3.8 16.6 - - - +
48A GLY 2.8 23.0 + - - -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 4.1 2.6 - - + +
14A ILE* 4.0 20.6 - - + -
17A LYS* 4.1 9.6 - - - +
18A LEU* 3.6 27.1 - - + -
31A PHE* 3.9 50.5 - - + -
41A ASP 2.8 17.7 + - - +
42A THR* 3.7 6.5 - - - +
43A VAL 3.2 0.2 - - - -
44A GLU* 1.3 74.9 - - - +
46A ILE* 1.3 74.4 + - + +
48A GLY* 3.1 1.7 + - - -
49A LEU* 2.9 45.5 + - + +
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 5.9 1.1 - - + -
42A THR* 3.2 24.5 + - + +
43A VAL* 3.8 8.1 - - + +
45A LEU* 1.3 88.1 - - + +
47A MET* 1.3 64.5 + - + +
49A LEU* 3.1 11.2 + - + +
50A GLU* 3.0 39.5 + - - +
57A ILE* 4.4 20.9 - - + +
62A ALA* 3.8 40.8 - - + +
65A ILE* 4.8 11.4 - - + +
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Residues in contact with MET 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 5.9 0.7 - - - -
43A VAL* 3.0 35.3 + - + +
44A GLU* 3.9 17.0 - - - +
46A ILE* 1.3 77.8 - - + +
48A GLY* 1.3 57.3 + - - +
50A GLU* 3.2 19.2 + - - +
51A ASP* 2.8 47.0 + - - +
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Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.7 18.1 - - - +
17A LYS* 3.9 15.5 - - - +
44A GLU 2.8 18.7 + - - -
45A LEU 3.1 2.4 + - - -
47A MET* 1.3 77.1 - - - +
49A LEU* 1.3 57.4 + - - +
51A ASP* 3.5 6.5 + - - +
52A GLU* 3.0 31.2 + - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.0 31.0 - - + -
13A VAL* 4.1 18.2 - - + -
14A ILE* 5.5 0.9 - - + -
45A LEU* 2.9 39.6 + - + +
46A ILE* 3.1 12.5 + - + +
48A GLY* 1.3 74.4 - - - +
50A GLU* 1.3 59.9 + - - +
52A GLU* 4.5 0.4 - - - -
53A PHE* 3.0 49.6 + - + +
55A LEU* 4.0 2.9 - - + +
57A ILE* 4.4 19.5 - - + -
65A ILE* 5.4 3.8 - - + -
71A ALA* 4.3 19.3 - - + -
75A ILE* 4.2 6.5 - - + -
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.0 23.7 + - - +
47A MET* 3.2 28.4 + - - +
49A LEU* 1.3 76.2 - - - +
51A ASP* 1.3 60.0 + - - +
54A GLY* 2.8 31.0 + - - -
55A LEU* 3.3 27.5 + - + +
56A GLU* 3.6 15.5 - - - +
57A ILE* 3.0 40.8 + - + +
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Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 5.7 1.7 - - - -
47A MET* 2.8 39.0 + - - +
48A GLY* 3.9 7.2 - - - +
50A GLU* 1.3 81.6 - - - +
52A GLU* 1.3 61.0 + - - +
54A GLY* 3.7 6.3 + - - -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS* 3.4 39.5 + - + +
12A ALA* 6.6 0.2 - - - -
13A VAL* 3.7 23.3 - - + +
48A GLY 3.0 19.5 + - - +
49A LEU 4.0 2.0 - - - +
51A ASP* 1.3 78.7 - - - +
53A PHE* 1.3 77.6 + - + +
54A GLY 3.9 0.2 + - - -
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.1 15.9 - - + -
6A ILE* 3.8 15.0 - - + -
9A LYS* 3.5 40.4 - - + -
10A VAL* 3.9 11.9 - - + -
49A LEU* 3.0 33.8 + - + +
52A GLU* 1.3 90.0 - - + +
54A GLY* 1.3 64.8 + - - +
55A LEU* 3.2 20.6 + - + +
75A ILE* 3.5 44.0 - - + -
79A LEU* 4.1 21.3 - - + +
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU 2.8 15.5 + - - -
51A ASP 3.7 5.4 + - - -
52A GLU 3.5 2.4 + - - -
53A PHE* 1.3 78.5 - - - +
55A LEU* 1.3 57.6 + - - -
56A GLU* 5.3 2.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il